Table 2.

Novel or very rare loss of function variants

ID	Variant (hg19)	Genotype	Gene	Variant (aa)a , b , c	Expected gene inheritance	Gene pLId (Samocha)	No. LoF per gene in ExAC
EP949	chr12:123433309‐T/‐	Hetero	ABCB9	p.N305 fs*35	Dominant	0.00	7
KIEL99	chr17:48736728‐C/T	hetero	ABCC3	p.R269X	Dominant	0.00	30
EUR578	chr19:13563750‐GGAAGGC/‐	Hetero	CACNA1A	p.A158 fs*6	Dominant	1.00	4
2012D09029	chrX:41414858‐G/A	Hemi	CASK	p.R584X	X‐linked	1.00	1
2007D04829	chr15:93527629‐TCAT/‐	Hetero	CHD2	p.I1046 fs*8	Dominant	1.00	5
2010D08930	chr15:93563370‐C/T	Hetero	CHD2	p.R1679X	Dominant	1.00	5
2008D06063	chr22:38694137‐G/‐	Hetero	CSNK1E	p.257 fs (minor transcripts)	Dominant	0.97	1
2012D20026	chrX:96603116‐G/C	Hemi	DIAPH2	c.2847‐1G>C (minortranscripts, missense in other rs775057363)	X‐linked	1.00	3
EUR585	chr3:132235289‐TT/‐	Hetero	DNAJC13	p.L1837 fs*48	Dominant	1.00	8
EG1761	chr6:5545412‐G/A	Hetero	FARS2	c.905‐1G>A (splice‐acceptor)	Recessive	0.00	10
D03/4526	chr11:134175014‐A/‐	Hetero	GLB1L3	p.A294 fs*2 (minor transcripts)	Dominant	0.00	22
D04/1316	chr11:134183917‐GA/‐	Hetero	GLB1L3	p.E555 fs*50	Dominant	0.00	22
2006D07509	chr16:56226254‐T/G	Hetero	GNAO1	p.L36X	Dominant	0.98	0
EP2822	chr14:67578576‐A/G	Hetero	GPHN	c.1315‐2A>G (splice‐acceptor)	Recessive	1.00	1
KIEL38	chr19:6731282‐G/T	Hetero	GPR108	p.Y454X	Dominant	0.00	16
EP1718	chr9:140056657‐C/T	Homo	GRIN1	p.Q556X	Dominant	0.97	4
2012D06376	chr1:245019802–/A	Hetero	HNRNPU	pV604 fs *24	Dominant	1.00	1
2010D12136	chrX:53265568‐G/T	Hemi	IQSEC2	p.Y1129X	X‐linked	0.98	1
EP1852	chr20:47990498‐G/T	Hetero	KCNB1	p.Y533X	Dominant	0.98	1
2012D18530	chr15:52664419‐T/A	Hetero	MYO5A	p.K907X	Dominant	0.99	16
EUR574	chr2:206617582‐G/T	Hetero	NRP2	p.G643X	Dominant	0.00	11
D04/2814	chr5:140603538‐G/‐	Hetero	PCDHB14	p.M154 fs*42	Dominant	0.00	12
2012D20026	chr3:126723726‐A/G	Hetero	PLXNA1	c.1620‐2A>G (splice‐acceptor)	Dominant	1.00	5
1011L	chr19:50365068–/CGACC	Homo	PNKP	p.A420 fs*49 (rs768847609)	Recessive	0.00	13
KIEL92	chr17:40278712‐C/T	Hetero	RAB5C	p.W130X (minor transcripts)	Dominant	0.83	1
KIEL38	chr2:166898868‐AAAGT/‐	Hetero	SCN1A	p.D702 fs*25	Dominant	1.00	2
2010D14485	chr20:1293995–/C	Hetero	SDCBP2	p.124‐125‐fs*33	Dominant	0.41	2
2006D07509	chr17:80218938–/A	Hetero	SLC16A3	p.296 fs (minor transcript)	Dominant	0.33	2
KIEL92	chr5:168123348‐G/‐	Hetero	SLIT3	p.T1017 fs*24	Dominant	0.99	11
EP2103	chr4:99064223‐G/A	Hetero	STPG2	p.Q27X	Dominant	0.00	18
2013D03222	chr16:2548263‐T/‐	Hetero	TBC1D24	p.H336 fs*11	Recessive	0.00	10
D02/2287	chr6:30123503‐C/T	Hetero	TRIM10	c.928 + 1G>A (splice‐donor)	Dominant	0.00	10
EP2805	chr4:39257574‐T/G	Hetero	WDR19	p.Y1036X	Dominant	0.00	20
2008D07479	chrX:48933578‐C/A	Hetero	WDR45	p.E155X	X‐linked dominant	0.97	0

Bold values indicate significant intolerance score.

^aFrameshift consequences calculated with SIFT (Hu and Ng 2012). Nonsense‐mediated decay predicted for all frameshifts except chr19:50365068–/CGACC, chr11:134175014‐A/‐ and chr22:38694137‐G/‐.

^bSome variants occur only in less well supported transcripts (“minor transcripts”).

^cFull description of variants including accession number in Tables S1–S3.

^dLoss‐of‐function intolerance score according to Samocha et al. (2014). Score ranges 0–1, with high scores meaning less tolerant.